Bottom Line:
Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins.Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense.Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed.

ABSTRACTThe Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed.

life-05-00783-f003: Alignment of leaders from CRISPR loci (Type I-A, PAM-CCN) of diverse members of the Sulfolobales showing significant levels of sequence identity over the first 230 bp from repeat 1, after which shared identity decreases (shaded area). Conserved sequence positions are indicated by asterisks and conserved sequence motifs are bracketed. The archaeal genome sequences are available at: https://www.ebi.ac.uk/genomes/archaea.html.

Mentions:
CRISPR loci consist of contiguous repeat-spacer units where the repeat is generally invariant, in size and sequence, for a given CRISPR locus whereas spacers usually all differ in sequence, and in length. Archaeal repeats fall into three size groups of about 24, 30 and 37 bp (Figure 2), differing by a little over half a turn of a DNA double helix, which may have some mechanistic significance for the adaptation, processing or interference reactions. Repeats of the Sulfolobales and many other crenarchaea are generally 24–25 bp while spacers lie mainly in the size range of 35–43 bp (Figure 2). Most CRISPR loci are preceded by leaders of approximately 200–400 bp which carry some low complexity sequence regions. An alignment of leader regions of Type I-A CRISPR loci (subfamily 1, see below) from diverse members of the Sulfolobales is shown in Figure 3. There is a significant degree of sequence conservation, including a few conserved motifs, for about 230 bp beyond the first repeat, after which sequence similarity gradually decreases.

life-05-00783-f003: Alignment of leaders from CRISPR loci (Type I-A, PAM-CCN) of diverse members of the Sulfolobales showing significant levels of sequence identity over the first 230 bp from repeat 1, after which shared identity decreases (shaded area). Conserved sequence positions are indicated by asterisks and conserved sequence motifs are bracketed. The archaeal genome sequences are available at: https://www.ebi.ac.uk/genomes/archaea.html.

Mentions:
CRISPR loci consist of contiguous repeat-spacer units where the repeat is generally invariant, in size and sequence, for a given CRISPR locus whereas spacers usually all differ in sequence, and in length. Archaeal repeats fall into three size groups of about 24, 30 and 37 bp (Figure 2), differing by a little over half a turn of a DNA double helix, which may have some mechanistic significance for the adaptation, processing or interference reactions. Repeats of the Sulfolobales and many other crenarchaea are generally 24–25 bp while spacers lie mainly in the size range of 35–43 bp (Figure 2). Most CRISPR loci are preceded by leaders of approximately 200–400 bp which carry some low complexity sequence regions. An alignment of leader regions of Type I-A CRISPR loci (subfamily 1, see below) from diverse members of the Sulfolobales is shown in Figure 3. There is a significant degree of sequence conservation, including a few conserved motifs, for about 230 bp beyond the first repeat, after which sequence similarity gradually decreases.

Bottom Line:
Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins.Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense.Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed.

ABSTRACTThe Sulfolobales have provided good model organisms for studying CRISPR-Cas systems of the crenarchaeal kingdom of the archaea. These organisms are infected by a wide range of exceptional archaea-specific viruses and conjugative plasmids, and their CRISPR-Cas systems generally exhibit extensive structural and functional diversity. They carry large and multiple CRISPR loci and often multiple copies of diverse Type I and Type III interference modules as well as more homogeneous adaptation modules. These acidothermophilic organisms have recently provided seminal insights into both the adaptation process, the diverse modes of interference, and their modes of regulation. The functions of the adaptation and interference modules tend to be loosely coupled and the stringency of the crRNA-DNA sequence matching during DNA interference is relatively low, in contrast to some more streamlined CRISPR-Cas systems of bacteria. Despite this, there is evidence for a complex and differential regulation of expression of the diverse functional modules in response to viral infection. Recent work also supports critical roles for non-core Cas proteins, especially during Type III-directed interference, and this is consistent with these proteins tending to coevolve with core Cas proteins. Various novel aspects of CRISPR-Cas systems of the Sulfolobales are considered including an alternative spacer acquisition mechanism, reversible spacer acquisition, the formation and significance of antisense CRISPR RNAs, and a novel mechanism for avoidance of CRISPR-Cas defense. Finally, questions regarding the basis for the complexity, diversity, and apparent redundancy, of the intracellular CRISPR-Cas systems are discussed.